AMBER Archive (2005)

Subject: RE: AMBER: new residue

From: Douali, Latifa (latifa.douali_at_pnl.gov)
Date: Wed Jul 27 2005 - 16:36:27 CDT

Yes, my monomer is a nucleotide
I mean "edit unit" not edit model"

Thank you

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of David A. Case
Sent: Wednesday, July 27, 2005 2:14 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: new residue

On Wed, Jul 27, 2005, Douali, Latifa wrote:

> I created new residue called RES.
> When I use the command "edit RES" in xleap, my monomer structure looks
> fine.
> I create a pdb file (using other software) for a polymer containing my
> monomer with the residue name (RES). When I do
> "> unit = loadpdb polymer.pdb"
> >edit model"
> The structure of my residue does not look planar as I expect. Using
> VMD to edit my polymer.pdb file, the structure looks fine.

This is weird. I'm not sure what you mean by "edit model", however. Is
"model" the name of some unit you have defined? What happens if you
type "edit unit" instead?

It may be that you have a non-standard PDB format, that VMD is somehow
interpreting correctly but LEaP is not. You might have to post the pdb
file. This doesn't seem like it has anything to do with the residue RES
definition: you can give LEaP a pdb file of completely unknown residues,
and it should still display it OK. You might try to break the pdb file
into pieces, and see what LEaP does with parts, in an attempt to debug
the problem.

> My question is how can I make nucgen recognize my new residue?

Where does nucgen fit in? Is your unspecified monomer a nucleotide?

...dac

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